Looking at the examples, I see that FHIR references are rarely used in CQL expressions for Measures. There's the occasional reference from MedicationRequest to Medication, but that's about it. "Prescriptions during an Encounter" is mostly expressed by an overlap in intervals of the 2 resources, not by checking for the existence of a reference from MedicationRequest to Encounter. 

It was argued that US Core doesn't mandate a lot of references. CQL is however not a US specification, and other countries do have core profiles with required references. CQL may have to rely on references in such contexts, 'dates' may not be present.

There are workarounds based on .id - but these won't always work. Please add native support for testing equivalence of a referenced resource and some other resource.